external-command.rb

require 'rubygems'
require 'eventmachine'

$stdout.sync = true
$stderr.sync = true

EM.run {
  
  EM.add_periodic_timer(0.1) {
    $stdout.write "stdout\n"
  }

  EM.add_periodic_timer(0.1) {
    $stderr.write "stderr\n"
  }
  
  EM.add_timer(1) {
    $stdout.write "stopping from stdout...\n"
    $stderr.write "stopping from stderr...\n"
    EM.stop
    
  }
  
  
}

popen3.rb

require 'eventmachine'

if RUBY_VERSION < "1.8.7"
  def __method__
    caller = /`(.*)'/
    Kernel.caller.first.split(caller).last.to_sym
  end
end

def log *message
  p [Time.now, *message]
end


module EventMachine

  class Process < EventMachine::Connection
  
    def initialize *args
      log __method__, args
    end
 
    def receive_data data 
      log __method__, data
    end
    
    def unbind
      log __method__
    end

  end

end


class MyStderr < EventMachine::Connection
  def initialize stderr
    @stderr = stderr
  end
  
  # Note: using receive_data here instead mysteriously breaks
  # this on linux....
  def notify_readable
    log __method__, @stderr.read
  end
end


def popen3 cmd, stdio_handler, stderr_handler
  new_stderr = $stderr.dup

  rd, wr = IO::pipe

  $stderr.reopen wr
  EM.popen cmd, stdio_handler
  EM.attach rd, stderr_handler, rd
  $stderr.reopen new_stderr

end


BEGIN { require 'rubygems' if __FILE__ == $0 }
if __FILE__ == $0
  file = "#{File.dirname(__FILE__)}/external-cmd.rb"
  cmd = "ruby #{file}"
  
  EM.run {
    
    EM.next_tick {
      $stderr.puts "stderr before"
      popen3 cmd, EM::Process, MyStderr
      $stderr.puts "stderr after"
    }
   
    EM.add_timer(2) {
      log :exit
      EM.stop
    }

  }

end

Note: using receive_data here instead mysteriously breaks

this on linux....

That's weird, using receive_data handler in MyStderr worked for me. Maybe you were getting some error and the stderr redirection shadowed it? With minor modification we end with a pretty comfy API:

http://gist.github.com/535644